Seed and pod decay significantly threaten to soybean yield and quality during the fruiting stage worldwide. Although, few previous studies partially explained the occurrence of Fusarium species on soybean seeds and pods, However, fungal diversity affecting soybean pods in Sichuan Province China, third-largest soybean cultivation region remains unknown. In this study, we identified pod-infecting fungal communities and evaluated their pathogenic potential on soybean seeds and pods. Using morphological indices and DNA barcode markers, we characterized Fusarium species, including F. verticillioides, F. incarnatum, F. equiseti, F. proliferatum, F. fujikuroi, F. oxysporum, F. chlamydosporum, and F. acutatum through Translation elongation factor gene (EF1-α) and RNA polymerases II second largest subunit (RPB2) gene analysis. Multi-locus phylogeny assay of Internal transcribed spacer (rDNA ITS), β-tubulin (β-tubulin), Glyceraldehyde 3-phosphate dehydrogenase (GADPH), Chitin Synthase 1 (CHS-1), Actin (ACT), Beta-tubulin II (TUB2) and Calmodulin (CAL) distinguished Colletotrichum species as C. truncatum, C. karstii, C. cliviicola, C. plurivorum, C. boninense, and C. fructicola. Pathogenicity assays revealed significant damage from Fusarium and Colletotrichum isolates on soybean pods and seeds, with varying isolation frequencies. Among them, F. proliferatum, F. acutatum, and F. verticillioides caused the most severe symptoms, while C. fructicola was most pathogenic, followed by C. truncatum, C. karstii, C. cliviicola, C. plurivorum, and C. boninense. These findings highlight emerging virulent pathogens responsible for soybean pod decay, paves a valuable foundation for developing resistant cultivars to manage pod associated diseases at the later growth stage of soybean.